Parse GlycoWorkbench Structures

Parse GlycoWorkbench (GWB/GWS) structure strings into a glyrepr::glycan_structure().

Usage

parse_gwb(x, on_failure = "error", progress = FALSE)

Arguments

x

A character vector of GlycoWorkbench strings. NA values are allowed and will be returned as NA structures.

on_failure

How to handle parsing failures. "error" aborts when a structure cannot be parsed. "na" returns NA at invalid positions.

progress

Whether to show a progress bar while parsing.

Value

A glyrepr::glycan_structure() object.

Details

GlycoWorkbench writes glycans from the reducing end towards the non-reducing ends. Residues include their anomer, configuration, and ring form, for example "--4b1D-Gal,p". Branches are enclosed in parentheses, and the structure is followed by mass options after $.

The parser normalizes the glycan tree to IUPAC-condensed notation before constructing the glycan structure. GlycoWorkbench substituent nodes such as "--6S" and "--9Ac" are retained as monosaccharide substituents. Mass options are ignored because they are not part of the glycan graph. Explicit open-chain residues (,o) are supported only for a reduced redEnd root; other open-chain forms cannot be represented by glyrepr.

See also

parse_iupac_condensed()

Examples

gwb <- paste0(
  "freeEnd--1b1D-GlcNAc,p(--6a1L-Fuc,p)",
  "--4b1D-Gal,p--3a2D-NeuAc,p$MONO,Und,0,0,freeEnd"
)
parse_gwb(gwb)
#> <glycan_structure[1]>
#> [1] Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> # Unique structures: 1